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LETTER: Analysis of the 5S RNA Pool in Arabidopsis thaliana: RNAs Are Heterogeneous and Only Two of the Genomic 5S Loci Produce Mature 5S RNA
- Catherine Cloix,
- Sylvie Tutois,
- Yasushi Yukawa,
- Olivier Mathieu,
- Claudine Cuvillier,
- Marie-Claude Espagnol,
- Georges Picard,
- and Sylvette Tourmente
Genome Res. January 1, 2002 12: 132-144; Published in Advance December 14, 2001, doi:10.1101/gr.181301
...Abstract One major 5S RNA, 120 bases long, was revealed by an analysis of mature 5S RNA from tissues, developmental stages, and polysomes in Arabidopsis thaliana . Minor 5S RNA were also found, varying from the major one by one or two base substitutions; 5S rDNA units from each 5S array...
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RESOURCE: Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans
- Jacqueline E. Schein,
- Kristin L. Tangen,
- Readman Chiu,
- Heesun Shin,
- Klaus B. Lengeler,
- William Kim MacDonald,
- Ian Bosdet,
- Joseph Heitman,
- Steven J.M. Jones,
- Marco A. Marra,
- and James W. Kronstad
Genome Res. September 1, 2002 12: 1445-1453; Published in Advance August 21, 2002, doi:10.1101/gr.81002
.... neoformans rDNA sequences revealed that BAC clones carrying rDNA genes were found in contig 7 for JEC21, but were not present in the 6528 clones from the H99 BAC library. This result may indicate that the rDNA sequences from H99 have a different organization of Hin dIII restriction sites that precluded...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...are the genomic regions adjacent to telomeres and often contain families of paralogous genes or pseudogenes, ribosomal DNA (rDNA) arrays, transposable elements, and other repeated sequences (Corcoran et al. 1988; Louis 1995; Kim et al. 1998; Fabre et al. 2005; Richard et al. 2013; Yue et al. 2017; Chaux-Jukic et...
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Research: Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
- Bo Li,
- Karl A.G. Kremling,
- Penghao Wu,
- Robert Bukowski,
- Maria C. Romay,
- En Xie,
- Edward S. Buckler,
- and Mingsheng Chen
Genome Res. October 2018 28: 1555-1565; Published in Advance August 30, 2018, doi:10.1101/gr.229716.117
...identical copies, accounting for >5% of plant s, for example, in Arabidopsis (Rogers and Bendich 1987). In spite of the high conservation level of their sequence and function, the copy number (CN) of rDNA is quite variable both between and within species (Gerlach and Bedbrook 1979; Rogers and Bendich 1987...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...that are associated with plant kinetochores remain unknown. The KARMA model makes specific predictions, including that CENH3 enrichment should correlate with the most homogenous repeat arrays, which has yet to be fully tested. It is also worth noting that other tandem repeat arrays, for example, rDNA, show similar...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...arrays of some RNA genes—especially clusters of rRNA genes collectively known as rDNA—are common in eukaryotes (Long and Dawid 1980; Cloix et al. 2000), tandem array organization of tRNAs (Bermudez-Santana et al. 2010) is unusual outside of the Entamoeba genus of Amoebozoa (Tawari et al. 2008), with only...
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Perspective: The genetics and epigenetics of satellite centromeres
- Paul B. Talbert and
- Steven Henikoff
Genome Res. April 2022 32: 608-615; Published in Advance March 31, 2022, doi:10.1101/gr.275351.121
...by BIR or microhomology-mediated BIR (Kockler et al. 2021). Initiation will frequently be out-of-register in a tandem array, with initiation behind the fork leading to expansion of the array, and initiation ahead of the fork leading to deletion (Fig. 1). In yeast rDNA arrays, expansion by BIR is favored...
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ARTICLE: The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes
- Bill Wickstead,
- Klaus Ersfeld,
- and Keith Gull
Genome Res. June 2004 14: 1014-1024; doi:10.1101/gr.2227704
...-bp repeat; ( B ) “reverse” 177-bp repeat; and ( C ) VSG -G4, VSG -S8, and an orphan rDNA promoter ( Zomerdijk et al. 1992 ). Partial maps were also produced from integration events into 177-bp repeats occurring on two ICs and one MBC ( D ). The IC of 345 kb was targeted using “forward” repeats...

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